It is not normal for command-line programs to have mutually-exclusive group flags. The reason for this is that a command-line may be assembled by more than one cooperating program. The standard way to deal with mutually exclusive flags is for the last flag given to take precedence over previous flags.

For example, consider the sort order of ls.

Removing groups would not only encourage authors to write more flexible command-line programs, but it would also make it easier to understand modes, which are very similar to groups. For example, look at the main menu of the info manual:

Group options:: Groups of mutual exclusive options

Mode options:: Mutual exclusive group of options

The sub-headings look very similar! Getting rid of groups would be an easy way to fix this confusion.